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Accueil > Teams > Fluorinated Molecules and Peptides of Therapeutic Interest - FLUOPEPIT > Molecular modelling

Molecular modelling

The goal of the “molecular modelling” team is to support rational design of new compounds targetting biological molecules and complexes, using various up-to-date in silico techniques, including quantum molecular calculations, all-atom molecular dynamics simulations, and coarse-grained modelling.

 Quantum molecular study of chemical reactivity:

- 1,3-dipolar cycloadditions (frontier molecular orbital theory). Collaboration with B. Crousse and T. Milcent (BioCIS).
- Additions to carbonyl/imines. Collaboration with D. Joseph and F. Lebideau (BioCIS).
- Electrophilic substitutions, metallation of heterocycles. Collaboration with L. Ferrié and Bruno Figadère (BioCIS).

 All-atom modeling of proteins conformation and association with small ligands:

- Study of the bacterial protein FtsZ : Molecular dynamics simulations of the monomer and dimer conformations. Molecular docking upon FtsZ of small peptides that inhibit its polymerization. Collaboration with N. Basdevant (University Evry) and P. Savarin (University Paris XIII).
- Homology modeling of the protein -sarcoglycan involved in genetic sarcoglycanopathies, a group of autosomal recessive muscle disorders. Collaboration with F. Leroys, I. Richard (Genethon) and N. Basdevant (University Evry).
- Enhanced molecular dynamics simulations (REMD and aMD) of amyloïdogenic peptides involved in neurodegenerative diseases In silico conception of peptidomimetic ligands that inhibit their polymerization. Collaboration with S. Ongeri (BioCIS).
- Homology molecular modeling of Leishmania guanosine-diphospho-D-mannose pyrophosphorylase. In silico conception of new anti-leishmanial molecules. Collaboration with S. Pomel, C. Cavé and P. Loiseau (BioCIS).

 Coarse-grained modeling of biomolecules assemblies:

  • Development of physics-based coarse-grained models of proteins and solvent in order to study their recognition and self-assemblies. Collaboration with N.
    Basdevant (University Evry) and D. Borgis (ENS).
  • Study by protein-protein docking and coarse-grained molecular dynamics of the interaction of the receptor CXCR7 with the CXCR4/CXCL12 signalling axis.
    Collaboration with F. Bachelerie (UMR 996).